Submodules updated

refresh-bio · Oct 3, 2024 · 43c26a5 · 43c26a5
1 parent 9a4e559
commit 43c26a5
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/3rd_party/clusty b/3rd_party/clusty
diff --git a/3rd_party/kmer-db b/3rd_party/kmer-db
diff --git a/3rd_party/lz-ani b/3rd_party/lz-ani
+0 −100		.github/workflows/deploy.yml
+3 −3		.github/workflows/main.yml
+36 −72		.github/workflows/self-hosted.yml
+0 −2		src/console.cpp
+4 −20		src/console.h
+117 −78		src/distances.cpp
+31 −20		src/distances.h
+0 −12		src/leiden.h
+20 −30		src/linkage_heaptrix.h
+2 −3		src/log.h
+1 −5		src/main.cpp
+3 −10		src/version.h
+0 −83		.github/workflows/deploy.yml
+4 −4		.github/workflows/main.yml
+18 −44		.github/workflows/self-hosted.yml
+3 −5		src/version.h
+0 −89		.github/workflows/deploy.yml
+0 −62		.github/workflows/main.yml
+0 −104		.github/workflows/self-hosted.yml
+67 −108		README.md
+0 −5,694		example/output/ani.aln.tsv
+133 −133		example/output/ani.tsv
+304 −0		libs/refresh/conversion.h
+0 −4,199		libs/refresh/conversions/lib/dragonbox.h
+0 −580		libs/refresh/conversions/lib/numeric_conversions.h
+0 −0		libs/refresh/file_wrapper.h
+0 −0		libs/refresh/memory_monotonic.h
+0 −0		libs/refresh/parallel-queues-common.h
+0 −0		libs/refresh/parallel-queues.h
+1 −1		makefile
+4 −92		src/defs.h
+14 −5		src/filter.cpp
+3 −25		src/filter.h
+2 −14		src/lz-ani.cpp
+59 −146		src/lz_matcher.cpp
+3 −30		src/lz_matcher.h
+243 −0		src/memory_monotonic.h
+36 −0		src/parallel-queues-common.h
+419 −0		src/parallel-queues.h
+39 −44		src/params.h
+2 −73		src/parser.cpp
+2 −10		src/parser.h
+2 −2		src/seq_reservoir.cpp
+4 −14		src/seq_reservoir.h
+2 −3		src/utils.cpp
+2 −2		src/utils.h
+0 −62		test/vir61.ani.ids.tsv
+0 −3,661		test/vir61.ani.tsv
+0 −568		test/vir61/NC_001271.1.fna
+0 −573		test/vir61/NC_001604.1.fna
+0 −548		test/vir61/NC_003298.1.fna
+0 −536		test/vir61/NC_004665.1.fna
+0 −539		test/vir61/NC_004777.1.fna
+0 −567		test/vir61/NC_007149.1.fna
+0 −570		test/vir61/NC_007456.1.fna
+0 −553		test/vir61/NC_008694.1.fna
+0 −557		test/vir61/NC_010807.1.fna
+0 −555		test/vir61/NC_011038.1.fna
+0 −571		test/vir61/NC_011040.1.fna
+0 −563		test/vir61/NC_011042.1.fna
+0 −591		test/vir61/NC_011043.1.fna
+0 −557		test/vir61/NC_011045.1.fna
+0 −552		test/vir61/NC_011085.3.fna
+0 −566		test/vir61/NC_011534.1.fna
+0 −590		test/vir61/NC_013647.1.fna
+0 −552		test/vir61/NC_013651.1.fna
+0 −562		test/vir61/NC_015159.1.fna
+0 −568		test/vir61/NC_015208.1.fna
+0 −563		test/vir61/NC_015249.1.fna
+0 −588		test/vir61/NC_015264.1.fna
+0 −551		test/vir61/NC_015271.1.fna
+0 −587		test/vir61/NC_015719.1.fna
+0 −553		test/vir61/NC_019416.1.fna
+0 −564		test/vir61/NC_019510.1.fna
+0 −604		test/vir61/NC_020483.1.fna
+0 −577		test/vir61/NC_021062.1.fna
+0 −572		test/vir61/NC_022744.1.fna
+0 −594		test/vir61/NC_023005.1.fna
+0 −569		test/vir61/NC_023548.1.fna
+0 −559		test/vir61/NC_023558.1.fna
+0 −563		test/vir61/NC_023576.1.fna
+0 −554		test/vir61/NC_023715.1.fna
+0 −580		test/vir61/NC_023736.1.fna
+0 −581		test/vir61/NC_024362.1.fna
+0 −561		test/vir61/NC_024379.1.fna
+0 −555		test/vir61/NC_025451.1.fna
+0 −562		test/vir61/NC_027292.1.fna
+0 −557		test/vir61/NC_027387.1.fna
+0 −563		test/vir61/NC_028655.1.fna
+0 −590		test/vir61/NC_028661.1.fna
+0 −576		test/vir61/NC_028688.1.fna
+0 −547		test/vir61/NC_028702.1.fna
+0 −562		test/vir61/NC_028772.1.fna
+0 −453		test/vir61/NC_028795.1.fna
+0 −598		test/vir61/NC_028800.1.fna
+0 −586		test/vir61/NC_028822.1.fna
+0 −581		test/vir61/NC_028863.1.fna
+0 −554		test/vir61/NC_028880.1.fna
+0 −589		test/vir61/NC_028977.1.fna
+0 −518		test/vir61/NC_029102.1.fna
+0 −564		test/vir61/NC_031018.1.fna
+0 −566		test/vir61/NC_031066.1.fna
+0 −562		test/vir61/NC_031092.1.fna
+0 −563		test/vir61/NC_031114.1.fna
+0 −568		test/vir61/NC_031115.1.fna
+0 −566		test/vir61/NC_031123.1.fna
+0 −570		test/vir61/NC_031258.1.fna
+0 −559		test/vir61/NC_031937.1.fna
+0 −581		test/vir61/NC_031943.1.fna